PosRange Class Reference

#include <pos_range.h>

Inheritance diagram for PosRange:

Public Member Functions
	PosRange ()
	PosRange (int From, int to)
int	start () const
int	end () const
int	size () const
bool	is_whole () const
bool	is_empty () const
bool	is_part () const
bool	has_end () const
bool	is_limited () const
bool	is_unlimited () const
bool	operator== (const PosRange &other) const
bool	operator!= (const PosRange &other) const
void	copy_corresponding_part (char *dest, const char *source, size_t source_len) const
char *	dup_corresponding_part (const char *source, size_t source_len) const
bool	contains (int pos) const
bool	contains (const PosRange &other) const
PosRange	after () const
PosRange	prior () const

Static Public Member Functions
static PosRange	empty ()
static PosRange	whole ()
static PosRange	from (int pos)
static PosRange	till (int pos)
static PosRange	after (int pos)
static PosRange	prior (int pos)

Detailed Description

Definition at line 28 of file pos_range.h.

Constructor & Destructor Documentation

PosRange::PosRange ( )

inline

Definition at line 33 of file pos_range.h.

Referenced by empty(), from(), and till().

PosRange::PosRange ( int  From, int  to  )

inline

Definition at line 34 of file pos_range.h.

References arb_assert.

Member Function Documentation

static PosRange PosRange::empty ( )

inlinestatic

Definition at line 51 of file pos_range.h.

References PosRange().

Referenced by after(), ED4_block::get_range_according_to_type(), prior(), and till().

static PosRange PosRange::whole ( )

inlinestatic

Definition at line 52 of file pos_range.h.

References from().

Referenced by BaseFrequencies::build_consensus_string(), FastAligner_start(), and ED4_block::get_range_according_to_type().

static PosRange PosRange::from ( int  pos )

inlinestatic

Definition at line 54 of file pos_range.h.

References PosRange().

Referenced by after(), intersection(), ED4_remap::screen_to_sequence(), and whole().

static PosRange PosRange::till ( int  pos )

inlinestatic

Definition at line 55 of file pos_range.h.

References empty(), and PosRange().

Referenced by prior().

static PosRange PosRange::after ( int  pos )

inlinestatic

Definition at line 57 of file pos_range.h.

References from().

Referenced by calculate_and_check_ranges().

static PosRange PosRange::prior ( int  pos )

inlinestatic

Definition at line 58 of file pos_range.h.

References till().

int PosRange::start ( ) const

inline

Definition at line 60 of file pos_range.h.

References arb_assert, and is_empty().

Referenced by alignCompactedTo(), alignToGroupConsensus(), BaseFrequencies::build_consensus_string_to(), calculate_and_check_ranges(), copy_corresponding_part(), ED4_setColumnblockCorner(), FastAligner_start(), AliChange::follow(), highlight_and_update(), intersection(), less_DistinctPosRange::operator()(), prior(), readCompactedSequence(), ED4_remap::screen_to_sequence(), ED4_remap::sequence_to_screen(), FINAL_TYPE< SEQTYPE >::set_range(), split_alignment(), chartable::SepBaseFreq::sub_and_add(), and BaseFrequencies::sub_and_add().

int PosRange::end ( ) const

inline

Definition at line 64 of file pos_range.h.

References arb_assert, and has_end().

Referenced by after(), BaseFrequencies::build_consensus_string_to(), ED4_setColumnblockCorner(), FastAligner_start(), AliChange::follow(), highlight_and_update(), intersection(), less_DistinctPosRange::operator()(), readCompactedSequence(), ED4_remap::screen_to_sequence(), ED4_remap::sequence_to_screen(), FINAL_TYPE< SEQTYPE >::set_range(), split_alignment(), chartable::SepBaseFreq::sub_and_add(), and BaseFrequencies::sub_and_add().

int PosRange::size ( ) const

inline

Definition at line 69 of file pos_range.h.

Referenced by alignCompactedTo(), BaseFrequencies::build_consensus_string(), copy_corresponding_part(), dup_corresponding_part(), AliChange::follow(), has_end(), is_empty(), and perform_block_operation_on_part_of_sequence().

bool PosRange::is_whole ( ) const

inline

Definition at line 71 of file pos_range.h.

Referenced by is_part(), ED4_manager::update_bases(), and ED4_manager::update_bases_and_rebuild_consensi().

bool PosRange::is_empty ( ) const

inline

Definition at line 72 of file pos_range.h.

References size().

Referenced by RangeList::add(), calculate_and_check_ranges(), contains(), ED4_setColumnblockCorner(), intersection(), is_limited(), is_part(), less_DistinctPosRange::operator()(), prior(), ED4_remap::screen_to_sequence(), PT_FamilyFinder::searchFamily(), ED4_remap::sequence_to_screen(), and start().

bool PosRange::is_part ( ) const

inline

Definition at line 73 of file pos_range.h.

References is_empty(), and is_whole().

Referenced by alignCompactedTo(), alignToNextRelative(), FastAligner_start(), readCompactedSequence(), Aligner::run(), and BaseFrequencies::sub_and_add().

bool PosRange::has_end ( ) const

inline

Definition at line 75 of file pos_range.h.

References size().

Referenced by after(), end(), and is_limited().

bool PosRange::is_limited ( ) const

inline

Definition at line 77 of file pos_range.h.

References has_end(), and is_empty().

Referenced by intersection(), and is_unlimited().

bool PosRange::is_unlimited ( ) const

inline

Definition at line 78 of file pos_range.h.

References is_limited().

Referenced by contains(), and ED4_remap::screen_to_sequence().

bool PosRange::operator== ( const PosRange &  other ) const

inline

Definition at line 80 of file pos_range.h.

bool PosRange::operator!= ( const PosRange &  other ) const

inline

Definition at line 81 of file pos_range.h.

void PosRange::copy_corresponding_part	(	char *	dest,
		const char *	source,
		size_t	source_len
	)		const

Definition at line 15 of file pos_range.cxx.

References arb_assert, size(), and start().

Referenced by alignToNextRelative(), and dup_corresponding_part().

char * PosRange::dup_corresponding_part	(	const char *	source,
		size_t	source_len
	)		const

Definition at line 27 of file pos_range.cxx.

References copy_corresponding_part(), and size().

Referenced by modsai_cb(), and read_sequence_region().

bool PosRange::contains ( int  pos ) const

inline

Definition at line 86 of file pos_range.h.

References is_empty(), and is_unlimited().

Referenced by RangeList::inverse().

bool PosRange::contains ( const PosRange &  other ) const

inline

Definition at line 114 of file pos_range.h.

References intersection(), and is_empty().

PosRange PosRange::after ( ) const

inline

Definition at line 91 of file pos_range.h.

References after(), empty(), end(), and has_end().

Referenced by after().

PosRange PosRange::prior ( ) const

inline

Definition at line 92 of file pos_range.h.

References empty(), is_empty(), prior(), and start().

Referenced by calculate_and_check_ranges(), and prior().

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The documentation for this class was generated from the following files:

• CORE/pos_range.h
• CORE/pos_range.cxx